I'm running with Mac, but I too had problems with trying to flash custom 2.1 ipsw (from Pwnage) to my device with iTunes 8. Following the normal upgrade process and then QuickPwn'ing totally did the trick. Just take iTunes out of the loop.
As long as Apple was going to keep farting around with trying to complete the SDK so developers aren't forced to jailbreak to write useful or interesting applications, you'd think they'd get OUT of the developer's hair and try to get to the point when we /could/ entirely rely upon AppStore for our needs. Way to go Apple!